Victorian taxpayers foot the $5,000-a-year bill for each patient, according to Associate Professor Telfer, who added that Commonwealth funding could free up hospital resources.

"What we could do is request that the GPs give ongoing prescriptions and injections," she said.

"That would take the load off the public hospital system … because they're not coming in every three months for an injection at the hospital."

Associate Professor Telfer and her team were responsible for drawing up new guidelines for treating transgender children and teenagers, which were recently published in the Medical Journal of Australia.

She said access to treatment was still lacking in many parts of Australia.

"Darwin, for example, doesn't have adequate services and doesn't have any services for children or adolescents and that severely disadvantages that population," she said.